A real-time PCR assay for Chlamydia pneumoniae in human atherosclerotic plaques by the use of novel probes and FRET LightCycler technology, is described. The assay proved particularly suitable for the specific and quantitative detection of a low DNA copy number in conventional PCR-negative samples. Among fifteen nested-PCR negative atherosclerotic plaques examined, our method detected three positive plaques containing 50(+/-3), 37(+/-2) and 24(+/-2) DNA copy number+/-SD in three independent experiments. Real-time PCR holds promise for C. pneumoniae quantitation in human atherosclerotic plaques.